OK, I am back after a bit of a delay. Had to go to Brazil for a couple of weeks on business, had a family surgery / health scare (OK now), etc.
An update on this - I am making better progress than I expected on the hard top and so am going to scratch the soft top for now. So I will likely just do the full external cage as close to the safari top as possible, since the consensus seemed to be that that top would be taller than the soft one, so the cage should work with either.
Since at some point the truck will hopefully be used for longer trips, the roof rack will be mounted to the top of the cage. The trailer idea is a good one but it is going to double the cost if I am going to do a cage anyway. A roof rack would be much cheaper, plus I could have an awning off the external cage. Pic of belt and suspenders on a Jeep:
I found this pic which gives an idea of the kind of mounts that could be attached to the capping and come out underneath the canvas (these come straight out; they could be angled down and curved to come out under it):